Defending the validity and significance of the new theorem “Fundamental Theorem of Natural Selection With Mutations, Part I: Fisher’s Impact

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– Bill Basener and John Sanford

 

Joe Felsenstein and Michael Lynch (JF and ML) wrote a blog post, “Does Basener and Sanford’s model of mutation vs selection show that deleterious mutations are unstoppable?”  Their post is thoughtful and we are glad to continue the dialogue. This is the first part of a response to their post, focusing on the impact of R. A. Fisher’s work.  Our paper can be found at: https://link.springer.com/article/10.1007/s00285-017-1190-x

First, a short background on our paper:

The primary thesis of our paper is that Fisher was wrong, in a fundamental way, in his belief that his theorem (“The Fundamental Theorem of Natural Selection”), implied the certainty of ongoing fitness increase. His claim was that mutations continually provide variance, and selection turns the variance into fitness increase.  Central to his logic was that collectively; mutations have a net zero effect on fitness.  While Fisher assumed mutations are collectively fitness-neutral, it is now known that the vast majority of mutations are deleterious. So mutations can potentially push fitness down – even in the presence of selection. Continue reading

Getting beyond abstruse theorems to science

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Joe Felsenstein recently posted a rebuttal of a critique of Fisher’s fundamental theorem of natural selection (FTNS).  The authors, Basener and Sanford, argue that if new mutation (missing from the original FTNS) is taken into account, the theorem shows that Darwinism is impossible rather than inevitable.  I agree with each point of Joe’s rebuttal.

Yet, I think that no discussion of this topic is complete without explaining that Fisher’s view, and more generally the original Modern Synthesis, is inadequate precisely because of the rejection of mutation-limited dynamics.

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Does Basener and Sanford’s model of mutation versus selection show that deleterious mutations are unstoppable?

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by Joe Felsenstein and Michael Lynch

The blogs of creationists and advocates of ID have been abuzz lately about exciting new work by William Basener and John Sanford. In a peer-reviewed paper at Journal of Mathematical Biology, they have presented a mathematical model of mutation and natural selection in a haploid population, and they find in one realistic case that natural selection is unable to prevent the continual decline of fitness. This is presented as correcting R.A. Fisher’s 1930 “Fundamental Theorem of Natural Selection”, which they argue is the basis for all subsequent theory in population genetics. The blog postings on that will be found here, here, here, here, here, here, and here.

One of us (JF) has argued at The Skeptical Zone that they have misread the literature on population genetics. The theory of mutation and natural selection developed during the 1920s, was relatively fully developed before Fisher’s 1930 book. Fisher’s FTNS has been difficult to understand, and subsequent work has not depended on it. But that still leaves us with the issue of whether the B and S simulations show some startling behavior, with deleterious mutations seemingly unable to be prevented from continually rising in frequency. Let’s take a closer look at their simulations.

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Natural Selection – Evolution Magic

Natural Selection is described as “the differential survival and reproduction of individuals due to differences in phenotype”. To this, some add “blind, mindless, and purposeless environmental process” that nonetheless is imagined turning random genetic mutations into superior new features enhancing descendants’ survivability (fitness). Accumulation of these features supposedly turns one lifeform into another over time. Natural Selection seeks to explain the appearance of design in nature without appealing to a designer.

This definition however fails the simplest test as different phenotypes survive different environments thus delinking phenotype from survivability. In a small farm, only organisms closely related to their wild cousins survive, but agribusinesses select for chickens with oversize breasts and research labs select for populations with specific genetic mutations requiring tight environments to survive. Although all these have different phenotypes, they do not possess an intrinsic phenotype “fitness” independent of the environment. In addition, who decides what is natural and what is not? Darwin considered domestication natural enough to include it as supporting argument. And as far as “blind, mindless, and purposeless”, all these are impossible to prove in addition to being utterly incompatible with the anthropic concepts of “better adapted” and “better fit”, both of which cannot be evaluated independent of survivability anyway.

Natural Selection is supposed to tie both ways survivability with phenotype, but this leaves out the environment which not only affects survivability directly, but also phenotype, itself a sum of genotype plus the environment, and even genotype that is a recurrent function of previous genotypes and the environment again. So in the end, survivability is a recurrent function of genotype, an infinite continuum of environments, and other unknown factors. While survivability can be measured as can be the individual genotype, measuring a population’s genotype is daunting at best, and the impact of the ever changing environment is simply impossible to evaluate. Phenotypes are impossible to define and measure in entirety even for one individual and, in addition, phenotype changes constantly from birth to adult to old age. We do see genetic mutations (unknowable if random) and we do know that, given a similar environment, extreme genotypes reduce survivability, yet we also know that a large variety of genotypes survive just fine in any population.

Fitness is never defined independently of survivability – this renders the fitness concept redundant especially since survivability can be measured while fitness cannot. Evolutionary Fitness is defined as the quantitative representation of natural and sexual selection (reproductive success) of a genotype or phenotype in a given environment. “Survival of the fittest” is interpreted as: “Survival of the form (phenotypic or genotypic) that will leave the most copies of itself in successive generations.” Not only is survivability the only measure, but survivability also changes with the environment.

Natural Selection is Intelligent Selection which is always done by an Intelligent Selector such as Darwin’s breeder which is an intelligent and willful player that takes intentional actions to reach preset goals. Predators, plants, birds, insects or bacteria, all show intelligence and the willful pursuit of predetermined goals. When interacting with the inert environment, organisms self-select rather than being selected by this environment. As soon as the organism dies and becomes part of the lifeless universe, all selection of that entity ceases.

Selection is limited to a narrow set of possible adaptations – what is not there, cannot be selected. Among the most common adaptations are body color/size/shape, hair type, antibiotic/chemical resistance, and behavior, and even these are limited in scope. Farmers would like to grow walking chicken breasts the size of hogs that grow much faster and come in various flavors, but this is not happening despite their best efforts. Antibiotic resistant bacteria still cannot survive extreme temperatures and chemical concentrations and their resistance decreases when the stimulus is removed. Rabbits cannot turn green when hopping over grass and white just over winter, despite the clear advantage such camouflage would bring. Size of tails, horns, beaks, trees, etc. are all stable over time as tradeoffs limit their growth. Human intelligence, flying, swimming, venom, and all other desirable capabilities remain restricted to specific organisms. Domestication has greatly helped mankind’s progress, but it has not changed the nature of the target animals and plants despite intensive efforts to accelerate their evolution. Instead, humans only enhanced the built in characteristics of domestic organisms and simply did without – a huge civilization disadvantage – when those plants and animals were unavailable. Hence, selection does not “design”, is limited in scope to a few available characteristics, and is reversed as soon as the selection pressure ends.

Extinct organism were not flawed and their features were not “selected away”. Most characteristics of the extinct survive just fine in current organisms of which some changed so little over time they are called living fossils. Sure, the mammal eye might provide superior vision to insect eye, but nothing comes for free and tradeoffs ensure both survive. Organisms that have completely vanished cannot be characterized as flawed and it would not take much imagination to see them thriving in a current landscape. The environment may have changed dramatically over time, however on a macro scale, the environment affected all organisms making the “natural selection” explanation highly doubtful regarding why some organisms survived in their old form, why some went extinct and why others would survive in a changed form. Humans and apes shared the same environment in Africa so common genotype would not have caused our dramatic differences just as lions are not that different than leopard, the cheetah and the others.

What if anything should replace Natural Selection? Humans have applied the most intensive and targeted selective pressure on us and others with great results for our existence. Yet we have not transformed even one organism into another – not even the lowly eColi after decades of laboratory work (Lenski). Our dogs are still basic canines and our cats are still basic felines, not much different than their wild cousins. If anything, we had to adapt to them rather than them to us. The finch, the moth, the antibiotic resistant bacteria are still the original organisms, their hailed changes having reverted or proven simple adaptations. We are no smarter, more powerful or longer living (in absolute) than out primitive ancestors. Selection is not transformative, much less creative.

Humans would apply the Natural Selection method if feasible. But we don’t because it isn’t. A Natural Selection software would use a random generator and a selection criteria to maximize survivability in an available niche. For instance, a family vehicle should optimize the transport function (survivability) given a set of environmental constraints (regulations) and an existing design as starting point. Random minute changes could be tested and retained if the transport function is improved. However, this method can only remove minor oversights but will never create any new designs. Any significant departure such as a new fuel, material or environment either results in a suboptimal design, or requires a cascade of changes to improve the survivability function. That is why the auto industry, like most other industries, introduces minor redesign annually and major revamps every few years. And while even the minor improvements must come in harmonized packages rather than one off (to reduce negative ramifications), in the absence of those major redesigns a firm would shortly go extinct.

Designs do not transform into better designs without crossing an inevitable optimization gap. Given a certain environment, once a design is optimized for a certain function, it becomes suboptimal as soon as the function, the structure, or the materials changes. Until the new design is optimized for that particular change, it remains inferior to an old design already optimized to that environment. Humans optimize new designs (with multidimensional differences from previous versions) conceptually before abruptly replacing old designs. A Darwinist biologic gradual design transition would thus be impossible hence never observed in nature. Had the compound eye been optimized first, a transition to non-compound eye would inevitably had to be suboptimal for a while and vice versa. Only if all eye designs had started from the same point, each following an independent path and at the same pace would we have so many different designs today, each optimized for its function. This however implies a coordinated original grand design incompatible with Darwinian evolution.

Pro-Con Notes

Con: What about organic design? Isn’t that natural selection at work?

Pro: No. This is just iterative optimization of a given design. In this case, the wing shape, the material, the environmental forces and the optimization target are all given. The algorithm will not generate a new wing shape or material and it will stop converging as soon as the environment is less than perfectly defined. In addition, this design is radically different from the previous one, and the next iteration will certainly be radically different than this one (no gradualism).

Con: You just don’t understand natural selection.

Pro: If “natural selection” were hard to understand it would not be taught to young children. Instead, “natural selection” is more like very bad street magic where the bus is covered with the cloth and we then are asked to imagine it disappeared without even removing the cloth and showing us the empty space.

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Atheism doubles among Generation Z

Good news from the Barna Group, a Christian polling organization:

Atheism on the Rise

For Gen Z, “atheist” is no longer a dirty word: The percentage of teens who identify as such is double that of the general population (13% vs. 6% of all adults). The proportion that identifies as Christian likewise drops from generation to generation. Three out of four Boomers are Protestant or Catholic Christians (75%), while just three in five 13- to 18-year-olds say they are some kind of Christian (59%).

This was particularly interesting…

Teens, along with young adults, are more likely than older Americans to say the problem of evil and suffering is a deal breaker for them.

…as was this:

Nearly half of teens, on par with Millennials, say “I need factual evidence to support my beliefs” (46%)—which helps to explain their uneasiness with the relationship between science and the Bible. Significantly fewer teens and young adults (28% and 25%) than Gen X and Boomers (36% and 45%) see the two as complementary.

The Falcon Heavy in binaural sound

I was in Florida last week for the inaugural Falcon Heavy launch, and though I wish I could do a mind meld and share the memories directly with you, the technology doesn’t yet exist.

Here’s the next best thing:

Destin is right. The sights are awesome, but it’s the sound that really makes the experience. Be sure to watch through to the point where the boosters come home to roost.

(Note for the impatient: Ignition happens around 3:20 into the video.)

How many different kinds of birds are there?

Once again I make an attempt to open the question of created kinds, or baramins, or whatever you want to call them: groups within which there is common descent but between which there is not. This is an opportunity for the creationists who frequent TSZ to school me on the subject.

I ask one simple question to begin the discussion: how many different kinds of birds are there? (It should be obvious why I chose birds, but the choice was, from a scientific standpoint, arbitrary.) As a followup, how can you tell? If there are indeed separately created kinds, I would think the divisions would be obvious. Would you agree, and why or why not? In any case, I’m not asking for precision; an answer within an order of magnitude will do.

Here’s my answer: 1; all birds belong to the same kind. In fact they form an infinitesimal fraction of a kind, since all life on earth is related. We have discussed the evidence many times here: nested hierarchy, etc. There are no joints at which kinds can easily be carved. How about you?

Has Feser proved that God is almighty, all-knowing, good, capable of free choice and loving?

In this post, I’ll be looking at chapter 6 of Dr. Edward Feser’s book, Five Proofs of the Existence of God, which deals with the nature of God, and I’ll be evaluating his arguments which purport to show that God is omnipotent, omniscient, good, capable of free choice and loving. I decided to begin by examining these “personal” attributes, because they’re the ones that really interest most people. Without these Divine attributes, any argument establishing that there exists an uncaused, fully actualized, necessary being, devoid of parts, whose essence is identical with its own act of existence could not be fairly called an argument for the existence of God, as such: it’s merely an argument for an Uncaused Cause.

My aim here is to evaluate Dr. Feser’s arguments in chapter 6, critically but fairly, in order to establish what they can tell us about God’s personal attributes, assuming that there exists an Uncaused Cause of the sort argued for by Feser in chapters 1 to 5 of his book. As we’ll see, Feser’s arguments for a personal Deity don’t prove much. All they establish is the following: (a) that everything depends on the Uncaused Cause, but not that it is capable of doing absolutely anything (or even anything which is consistent with its nature); (b) that universals exist in the Mind of the Uncaused Cause (a conclusion Feser argues for in chapter 3), but not that it actually knows any true propositions, let alone all true propositions; (c) that the Uncaused Cause is one-of-a-kind and free from defects, but not that it is benevolently disposed towards us; (d) that the Uncaused Cause is self-fulfilled and complete as a Being, but not that it is capable of free choice; and (e) that the Uncaused Cause brings about whatever is necessary for things to exist – whether it does so intentionally is another matter, however – but not that it cares about what happens to those things in the future, let alone that it cares about our future. After reviewing each section, I’ll discuss how Feser’s arguments could be strengthened, to make them more powerful. In addition, I’m going to throw in a bonus gift: I intend to show that Feser’s strong doctrine of the Purely Actual Actualizer (which he argues for in chapter 1) is false and untenable, before arguing that there is no need for classical theists to hold it: all they need to maintain is that God’s existence involves no actualization of potential (even if His activities do).

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Immortal Soul Anyone?

At Evolution News and other, Dr. Michael Egnor has been writing extensively on the subject of mind, thought, consciousness and soul: here,  here, here , here , here and here.
It seems that all his efforts have been concentrated on the critic of the materialistic views of the origins the mind, thoughts and consciousness. To make the long story short, Dr. Egnor is convinced that with the exception of one type of thoughts, where some thought patterns have been detected in human brain by MRI, EEG etc., other types of thoughts, such as abstract thoughts, can’t be explained in materialistic terms and therefore they are directly or indirectly a solid proof of the existence of an immaterial soul or the Thomistic Dualism dogma propagated Thomas Aquinas  in the 13th century…

While there maybe a third explanation for this phenomenon, such as quantum consciousness/mind/thoughts, which I had already covered here , in this OP however, I would like to focus on another aspect of this issue:

Where did the idea of the immortal soul come from in the first place? Continue reading

Is Photosynthesis irreducibly complex?

Feedback from this site has proven most valuable, when constructing worksheets for the Science classroom,

I have attempted a new tack – by bearding the creationist lion in the classroom den.

I offer the following for everyone’s perusal.

I welcome correction or suggestions for improvement.

https://www.dropbox.com/s/djr9c4e2lymsb33/Irreducible%20complexity%20of%20photosynthesis.docx?dl=0

with best and grateful regards

Feser’s predestinationism and his bizarre claim that God’s knowledge is non-propositional

Today, I’m going to start looking at chapter 5 of Dr. Edward Feser’s Five Proofs of the Existence of God. I thought I’d begin with Feser’s take on Divine foreknowledge and free will. To cut a long story short: Feser is a predestinationist who professes at the same time to believe that humans possess genuine free will. In order to reconcile these beliefs, he proposes an analogy which at first seems plausible, but which ultimately collapses because it completely ignores our personal relationship with our Creator. To make matters worse, Feser holds that God knows everything that happens in this world, non-propositionally. He proposes another analogy to explain how this might be, but at most, it merely explains how God might know creatures; it fails to explain how He knows what they get up to. I conclude that not only is Feser’s account of God’s foreknowledge incoherent, but his account of how God knows any fact whatsoever about the world is also unintelligible.

This will be a much shorter post than my last one, so there’s no need to crack open a beer (at least, not yet). I’ll explain the picture of Mia Farrow shortly.

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18 really dumb (and not-so-dumb) objections to arguments for the existence of God

On Thursday, I received two books which I had previously ordered from Amazon: Five Proofs of the Existence of God by philosopher Edward Feser, and The Resurrection: A Critical Inquiry by Michael Alter, a Jewish author who claims to have discovered no less than 120 contradictions in the New Testament accounts of Jesus’ Resurrection. I’ve also ordered Did Jesus Really Rise From The Dead?: A Surgeon-Scientist Examines the Evidence by Dr. Thomas Miller (a surgeon who is also the author of more than 200 scientific papers and the editor of three textbooks on surgical physiology), but that book hasn’t arrived yet. I’m going to blog about all of these books, but today, I’d like to begin by discussing Dr. Edward Feser’s book. Just to be clear: Feser’s five proofs are not the same as St. Thomas Aquinas’ Five Ways. They are taken from the writings of five different philosophers: Aristotle, Plotinus, Augustine, Aquinas and Leibniz. Feser refers to the arguments put forward by Aristotle and Plotinus, in particular, as cosmological or “First Cause” arguments, although Aquinas also advances a First Cause argument of his own. Leibniz argues to the existence of an ultimate explanation for the existence of contingent beings, using the Principle of Sufficient Reason. Augustine’s argument is the odd one out: it seeks to establish the existence of a necessarily existing intellect which grasps all abstract objects.

Feser’s book has received glowing reviews from four professors of philosophy, one of whom (J.P. Moreland) described it as “a must-read for anyone interested in natural theology.” Over at Secular Outpost, Bradley Bowen seems to agree. He concludes Part 1 of his ongoing review of Feser’s book as follows:

I don’t know at this point whether any of Feser’s arguments are good or bad, valid or invalid, sound or unsound, but even if they are all weak and defective arguments, I am still very grateful to Feser for providing a case for God that meets some basic intellectual requirements for making a reasonable case for God. Unlike the cases for God by Geisler and Kreeft, Feser’s case is NOT a Steaming Pile of Crap, and it is a great pleasure to consider a case that at least has the potential to be a reasonable and intelligent case for God.

Instead of reviewing Feser’s book from start to finish, I’m going to begin with the final chapter, where Feser refutes eighteen common objections to the arguments he presents for the existence of God. Philosopher Stephen T. Davis described this chapter as a gem, adding that “it alone is worth the price of this excellent work.” I’m going to enumerate these objections and quote some very brief excerpts from Feser’s replies. As we’ll see, most of these objections are puerile and idiotic, but a couple of them are not so ridiculous, and warrant further examination.
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1. Evolution or Design? Duons

Have you ever tried writing palindromes? How about writing phrases that can be read the same way in either direction? Here are some examples:
A man, a plan, a canal: Panama
Live not on evil
Was it a car or a cat I saw
These sentences were no doubt designed…
Can you imagine writing a book that can be read forwards and backwards containing 2 different stories that made sense? Not an easy task…

Watch the video and pay special attention to the following examples:

  1. Alternative splicing of RNA that produces multiple proteins from one gene
  2. Duons – Overlapping sequences that code for both protein expression and transcription factor binding sites simultaneously
  3. Dual coding genes in which one sequence is read in multiple frames to produce completely different protein

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Finally some good news: U.S. Belief in Creationist Views at New Low

Highlights from Gallup News:

-38% say God created man in present form, lowest in 35 years
-Same percentage say humans evolved, but God guided the process
-Less-educated Americans more likely to believe in creationism

Higher education levels are associated with less support for creationism and higher levels of belief in the evolutionary explanation for human origins.

http://news.gallup.com/poll/210956/belief-creationist-view-humans-new-low.aspx

The Search Problem of William Dembski, Winston Ewert, and Robert Marks

Introduction to Evolutionary Informatics, by Robert J. Marks II, the “Charles Darwin of Intelligent Design”; William A. Dembski, the “Isaac Newton of Information Theory”; and Winston Ewert, the “Charles Ingram of Active Information.” World Scientific, 332 pages.
Classification: Engineering mathematics. Engineering analysis. (TA347)
Subjects: Evolutionary computation. Information technology–Mathematics.1

Search is a central term in the work of Dr. Dr. William Dembski jr, Dr. Winston Ewert, and Dr. Robert Marks II (DEM): it appears in the title of a couple of papers written by at least two of the authors, and it is mentioned hundreds of times in their textbook “Introduction to Evolutionary Informatics“. Strangely – and in difference from the other central term information, it is not defined in this textbook, and neither is search problem or search algorithm. Luckily, dozens of examples of searches are given. I took a closer look to find out what DEM see as the search problem in the “Introduction to Evolutionary Informatics” and how their model differs from those used by other mathematicians and scientists.
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To Basener and Sanford: This is the 21st Century

What is The Skeptical Zone, William Basener and John Sanford? Why should you care?

The Skeptical Zone is where a couple of distinguished biologists, Joe Felsenstein and Michael Lynch, have dignified a recently published article of yours with a response. That is all you need to know. If they had responded on the back of a cereal box instead, providing you with a form to clip, then it would have behooved you to clip the form, fill it out, and send it, along with a self-addressed, stamped envelope, to their post office box in Battle Creek, Michigan.

Of course, I am dating myself — and also you. That is just the point. You ought to know that, even as the computer enables studies that were impossible when Ronald Fisher dubbed a not-so-fundamental result of his the Fundamental Theorem of Natural Selection, it enables interaction with domain experts in ways that were impossible in Fisher’s time. We are well into the 21st Century, and no one under the age of 50 will find credible any reason you might offer for declining to engage Joe in this forum. You can ignore all of the riff-raff, myself included, and interact with the scientist who happened, about the time that your paper addressing Fisher’s theorem was published, to address the theorem in the 37th Fisher Memorial Lecture (via video link, I might add).

The prospects for resolving some points, and arriving at a degree of agreement, are much better in a modern exchange of comments than in an old-fashioned exchange of essays. One aspect of The Skeptical Zone makes it particularly appealing in discussion of mathematical models: you can enter stuff like \LaTeX between two dollar signs, and cause readers to see stuff like \LaTeX. It’s a miracle!

Thomas Metzinger on ‘mental autonomy’

An interesting article in Aeon by Thomas Metzinger:

Are you sleepwalking now?

Given how little control we have of our wandering minds, how can we cultivate real mental autonomy?

He develops a metaphor of conscious thoughts as dolphins that leap from the water of unconscious processing into the air of conscious awareness, and asks:

The really interesting question then becomes: how do various thoughts and actions ‘surface’, and what’s the mechanism by which we corral them and make them our own? We ought to probe how our organism turns different sub-personal events into thoughts or states that appear to belong to ‘us’ as a whole, and how we can learn to control them more effectively and efficiently. This capacity creates what I call mental autonomy, and I believe it is the neglected ethical responsibility of government and society to help citizens cultivate it.